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- PDB-7r3n: mouse Interleukin-12 subunit beta - p80 homodimer in space group ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r3n | ||||||
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Title | mouse Interleukin-12 subunit beta - p80 homodimer in space group P21 crystal form 3 | ||||||
![]() | Interleukin-12 subunit beta | ||||||
![]() | CYTOKINE / HOMODIMER / ANTAGONIST / FIBRONECTIN / SECRETED GLYCOPROTEIN | ||||||
Function / homology | ![]() Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of T-helper 1 type immune response / positive regulation of smooth muscle cell apoptotic process / natural killer cell activation / T-helper cell differentiation / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / response to UV-B / cytokine receptor activity / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / defense response to protozoan / positive regulation of interleukin-17 production / positive regulation of interleukin-10 production / : / immunoglobulin mediated immune response / negative regulation of protein secretion / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / negative regulation of inflammatory response to antigenic stimulus / positive regulation of interleukin-12 production / negative regulation of smooth muscle cell proliferation / cytokine activity / endosome lumen / growth factor activity / cellular response to type II interferon / cytokine-mediated signaling pathway / Golgi lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell migration / cellular response to lipopolysaccharide / defense response to virus / defense response to Gram-negative bacterium / cell population proliferation / cell surface receptor signaling pathway / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / protein-containing complex binding / cell surface / extracellular space / extracellular region / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bloch, Y. / Savvides, S.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Around she goes: the structure of mouse Interleukin-12 p80 Authors: Bloch, Y. / Savvides, S.N. #1: ![]() Title: Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis. Authors: Kozak, S. / Bloch, Y. / De Munck, S. / Mikula, A. / Bento, I. / Savvides, S.N. / Meijers, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 573.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6smcC ![]() 6sp3C ![]() 7purC ![]() 6sffS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38282.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Residues [1-22] encode a secretion signal which is should have been co-translationally removed. Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.45 % / Description: parallelogram shaped plate |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6 Details: BCS screen, 0.2M sodium formate, 0.1M sodium phosphate pH 6.0, 17% PEG Smear Medium, 10% Glycerol. Cryoprotected with up to 27.5% PEG Smear Medium prior to vitrification. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→111.67 Å / Num. obs: 35159 / % possible obs: 99.1 % / Redundancy: 4.64 % / Biso Wilson estimate: 89.24 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.16 / Net I/σ(I): 8.09 |
Reflection shell | Resolution: 3.1→3.29 Å / Redundancy: 4.66 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 5551 / CC1/2: 0.526 / Rrim(I) all: 1.732 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6sff Resolution: 3.16→61.03 Å / SU ML: 0.4417 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6817 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 117.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.16→61.03 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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